Since your post is in the Standards & Accessibility (tagged PDF) discussion area, I am guessing that your objective is to tag the reference and footnote or endnote to ensure accessibility by assistive technology users. A good practice is to nest the reference number in a Reference tag, and the footnote or endnote in a Note tag, then position the Note as close as practical to the Reference in the tag structure without disrupting the reading order. In this case the tags would look something like this:
...Obstructive sleep apnea (OSA) is associated with increased reduced slow wave sleep.
......1. Ng AK, Guan C. Impact of obstructive sleep apnea on sleep-wake stage ratio.
The current version of the Matterhorn Protocol requires the Note tag to have a unique ID in the Object Properties. The ID is not used for anything though, and the requirement will reportedly be removed from future versions.
Hope this helps.
a 'C' student